Abstract Head and Neck Cancer (HNC) is an aggressive disease, often treated with combinations of radiation, targeted therapy and immunotherapies. Immune checkpoint inhibitors for patients with HNC have shown modest clinical response rates of ~20%. It is unclear how radiation may potentiate the impact of immunotherapies in combination strategies. Pre-clinical models have found that radiation-induced mutational burden and HLA expression may synergize with immunotherapies to improve response rates. Unfortunately, there are limited biomarkers available to evaluate phenotypic and gene expression changes induced by combination strategies. Circulating tumor cells (CTCs) have shown clinical value in numerous solid tumors, and have potential in HNC as a liquid biopsy to evaluate these treatment induced molecular alterations. In this report, we integrate CTC capture using EGFR as a target antigen for phenotype and gene expression analysis in mouse models and samples from patients with HNC. The efficiency and specificity of microfluidic EGFR CTC capture was verified in vitro using serial dilutions of HNC cell lines: two expressing EGFR (SCC6 and MOC2-huEGFR) and one without (MOC2). Mouse models were used to confirm ex vivo EGFR capture by IV injection of calcein-stained MOC2-huEGFR cells, followed by blood draw <1 minute post-injection. CTCs were then isolated and characterized from blood drawn from patients with HNC using the same microfluidic capture. The median capture efficiencies for SCC6 and MOC2-huEGFR cells were 100% and 87%, respectively, over a range of 5-100 target cells (R2= 0.9999). No untransfected MOC2 cells were captured at the 100 cell dilution level. An average of 10 cells was captured from the blood of mice injected with 1x10^6 MOC2-huEGFR cells; detectable with both single-cell microscopy and RT-qPCR for EGFR mRNA expression. CTCs were successfully detected in blood samples from patients with HNC and identified with single-cell expression of PD-L1 and HLA I as potential biomarkers of response and resistance. These results demonstrate the single-cell sensitivity for the evaluation of both protein and mRNA biomarkers on HNC CTCs. The high levels of accuracy and sensitivity achieved with the EGFR-based capture showcase the potential for HNC drug development using murine models of metastatic HNC. Successful detection of HNC CTCs has led to the integration of this assay in clinical trials for patients with this disease. Future directions include evaluation of additional CTC protein and mRNA biomarkers in murine models and samples from patients with HNC. Citation Format: Matt C. Mannino, Caroline P. Kerr, Jennifer L. Schehr, Shuang G. Zhao, Zachary S. Morris, Joshua M. Lang. Microfluidic characterization of circulating tumor cells from mouse models and patients with head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5121.